Systematics: Tree of Life http://tolweb.org/tree/phylogeny.html 1) Taxonomy: Classification and naming of organisms Hierarchical nomenclature with taxonomic categories (kingdom, phylum, class, order, family, genus, and species) 2) Phylogenetic analysis: The study of evolutionary relationships among species a. Under common decent, hierarchical classification reflects true genealogical relationships Tree of Life http://tolweb.org/tree/phylogeny.html

Phylogenetic Analysis Species 1 a b c d e f g h i j 0 0 1 1 1 0 0 0 0 0 Species 2 a b c d e f g h i j 0 0 1 0 0 1 1 1 1 0 Species 3 a b c d e f g h i j 0 0 1 0 0 1 1 0 0 1 Species 4 a b c d e f g h i j 1 1 0 0 0 0 0 0 0 0 i1 j1 h1 e1 Ancestor 3 (node) d1 g1 f1 b1 shared characters a1 Ancestor 2 (node) 1 2 3 4 1 - 4 5 5 2 1 - 7 3 3 1 3 - 4 4 0 0 0 - c1 shared derived characters Ancestor 1 a b c d e f g h i j 0 0 0 0 0 0 0 0 0 0

Phylogenetic Terms i1 j1 e1 h1 d1 g1 f1 b1 a1 c1 Species 1 Species 2 Species 3 Species 4 i1 j1 e1 h1 Ancestor 3 d1 g1 f1 b1 Ancestor 2 a1 monophyletic group: set of species that share a common ancestor. synapomorphy: shared derived character state. autapomorphy: uniquely derived character c1 Ancestor 1

The identification of synapomorphies help define nested series of monophyletic groups.

Phylogenetic Analysis Species 1 a b c d e f g h i j 0 1 1 0 0 0 1 1 0 1 Species 2 0 1 1 1 1 1 0 1 0 0 Species 3 0 1 1 1 1 1 1 0 1 1 Species 4 1 0 0 0 0 0 0 0 0 0 Ancestor 1 Ancestor 2 Ancestor 3 h1 g1 c1 f1 i1 j1 a1 b1 j0 e1 d1 shared characters 1 2 3 4 1 - 5 5 4 2 3 - 6 3 3 4 5 - 4 4 0 0 0 - shared derived characters

Phylogenetic Terms i1 j0 g1 h1 h1 f1 g1 e1 d1 a1 j1 c1 b1 Species 1 Species 2 Species 3 Species 4 j0 i1 g1 h1 h1 f1 Ancestor 3 g1 e1 d1 a1 Ancestor 2 j1 homoplasy: when two species share a derived character state because of convergent evolution or evolutionary reversal, but not because of common descent. convergent evolution: independent evolution of a derived character state in two or more taxa. c1 b1 Ancestor 1

Example: Wings in insects, birds, and bats Types of Homoplasy Convergence: Shared derived similarities, that are not based on common origin (i.e. homology ), but on an independent origin in different taxa. Example: Wings in insects, birds, and bats Reversal :The secondary presence of an apparently ”ancestral” character state. Example: Aquatic mode of life for fish, terrestriality for tetrapods, reversal to aquatic life in whales

Homoplasy: Common in DNA sequence data Homoplasy: Common in DNA sequence data. Each nucleotide position defines a separate character

Homoplasy - independent evolution Loss of tails evolved independently in humans and frogs - there are two steps on the true tree Lizard Human TAIL (adult) absent present Frog Dog

Homoplasy: Misleading evidence of phylogeny If misinterpreted as a synapomorphy, the absence of tails would be evidence for a wrong tree: grouping humans with frogs and lizards with dogs Human Lizard TAIL absent present Frog Dog

Homoplasy: Reversal True tree Wrong tree Reversals are evolutionary changes back to an ancestral condition As with any homoplasy, reversals can provide misleading evidence of relationships True tree Wrong tree 1 2 3 4 5 6 7 8 9 10 1 2 7 8 3 4 5 6 9 10

So how do we construct trees with a sample of homologous characters? How do we sort out phylogeny from a mixture of signal (synapomorphies) and noise (homoplasy). Cladistic methodology (Willi Hennig) utilizes the principle of parsimony. Parsimony= The tree that requires the fewest number of evolutionary changes or steps to explain the data is preferred.

Tree Reconstruction with Parsimony

Tree Reconstruction with Parsimony Nucleotide substitution = evolutionary step

Tree Reconstruction with Parsimony

Tree Reconstruction with Parsimony Character 2 Tree 1 Tree 2 Tree 3 I(A) III(A) I(A) II(G) I(A) II(G) II(G) IV(G) III(A) IV(G) IV(G) III(A) or or I(A) III(A) I(A) II(G) II(G) IV(G) IV(G) III(A)

What to do when some characters tell you one thing and others tell you something else (Homoplasy)? Parsimony with Multiple Characters The most parsimonious pattern of character change is noted for each character separately, for each tree. The number of changes is summed across characters for each tree. The preferred tree is the one that implies the fewest overall character changes. 1 2 3

Tree 1 is favored under the criterion of Parsimony

Parsimony Advantages: Disadvantages: Simple method - easily understood operation Does not seem to depend on an explicit model of evolution Should give reliable results if the data is well structured and homoplasy is either rare or widely (randomly) distributed on the tree Disadvantages: Doesn’t always provide the best estimate of phylogeny Maximum likelihood Bayesian analysis